Is it worth farming to get the chocolate CE's?

Is CE Exp worth the time and AP to you? Or would you rather use it for farming embers/QP/mats? Since, as you said, there's no real way to quantify its cost, it would depend on you at the end.

One CE from the shop gives 30000 exp which is a similar amount to what you can get from a few multi-rolls on the FP banner. Not really worth it IMO. But that depends on how dire your FP situation is. ;) I have more than I can use of them..

Personally, I don't think so. I don't care about collecting them or the cut-scenes, and the amount of CE you get from them you'll get in probably 3 days of so from the FP gacha. They cost about half of one Royal farming run, and I have a lot better things to do with my coins. If you end up having to use apples to farm what you want out of the shop at the end because of that, that to me is really a waste.